Starfleet Command is attempting to contain a rapidly growing Federation mutiny in the Sagittarius Arm. Every Federation starship set to discover the nature of the problem has also mutinied and joined the Klingons. To avoid the mutiny spreading to the entire Federation, Starfleet plans to wrap the entire area in a Klein Sphere, sealing it off forever.
In a last attempt to find out what is happening, Starfleet sends in the Enterprise before the Sphere is set up. Its five year mission is to attempt to discover what is causing the defections, and hopefully stop them. If you fail in your mission, the Sphere will be made permanent, if you succeed the Sphere will be dropped, avoiding a potential war with the Romulans.
The game is basically a graphical adventure with some real-time combat and piloting. The game progresses by flying to planets, beaming down on them, and retrieving any items you find. There are several possible solutions to the game, with clues found along the way.